Protein Folding Activity

For this activity you will need one piece of printer paper, scissors, and tape or a stapler.
(Notebook paper will do but do not use the parts with the holes.)

___ First, cut the paper into about 8 long strips. Each strip will be about 1 inch wide.

___Then, divide the strips into two piles. Take the strips in one pile and tape them together at
the ends, then repeat with the second pile. Now you will have two long strips of paper.

___ Use a pencil and ruler to make a line about every two inches on each strip.

___Using an online source or your textbook, write the 3 letter code for an amino acid on each
section of your strips. Be random in your choices! (If you are in the mood to be artistic, you
could make each AA a different color!) Your two strips can have the same amino acid sequence
or be different. As you write the names, also note if the side chain of the amino acid is:

Polar
Nonpolar
Charged +
Charged -
Or if it has a Sulfur in the side chain.

Ex:

*Answer all questions in an electronic document or on paper, not within the worksheet.
For all questions, RTQAPOYA! (Rephrase The Question As Part Of Your Answer.)
For example, if the question asked, “What is your favorite color?” :

DO NOT answer: “Blue.” DO ANSWER: “My favorite color is blue.”

Q1: Which level of protein structure have you just created: 1°, 2°, 3°,4° ? Explain.

This represents primary protein structure, because that is the order of the amino
acids in the polypeptide chain.

Q2: What type of bonds are represented by the lines between your amino acids?
Explain.

The lines represent peptide bonds.

___Next, let’s mimic secondary structure. Take one strip and fold it accordion style by just
folding it back and forth every few inches. Take the other strip and wrap it around a pencil to
make it like a loose spiral. (Don’t worry if it isn’t perfect. You are just making a simple model!)

Q3: What are the names for each of these

shapes? (Hint: they include Greek symbols)

The accordion style represents beta pleats and the spiral represnts the alpha
helix shape.

Q4: What type of bonds are causing these shapes? Which part of the amino
acids are involved?

These shapes are caused by hydrogen bonds. They are created between the
repeating parts of the polypeptide backbone.

___ Now it is time to model tertiary structure. For each strip, make several (you decide how
many) bonds/connections. Find two or more AAs that will interact and connect them with tape
or staples following these guidelines:
In the watery environment of the cell:
*Polar amino acids will want to have contact with other polar amino acids
* Nonpolar amino acids will want to form hydrophobic pockets with each other toward the
interior of the protein, away from the water.
* Charged (acidic and basic) amino acids will be attracted to opposite charges.
* Cysteine amino acids will form disulfide bridges with each other

Q5: List 3 types of connections you made and list the AAs involved. For
example: I connected two METs because they are nonpolar.

Answers will vary depending on which amino acids you chose.

Q6: Which parts of the amino acids are involved in the bonds you made for the
tertiary structure?

The bonds that create the tertiary structure are created by the interactions
between the side chains (R groups) of the various amino acids.

___ Finally, decide how to model quaternary structure. Not all proteins have quaternary
structure, but yours does. You rock!

Q7 What does denature mean? Name two things that might denature a real
protein, then name two things that might denature your paper protein.

Denature means to break down, the protein starts to unravel and loses its shape.
Things that can denature a real protein could be an extreme pH, temperature, or
salt concentration.

Q8 A mutation is a change in the DNA sequence. If the DNA sequence that

coded for your protein was changed, it might alter the structure by changing
which amino acid is in a certain spot. Give one example of a bond you created
that would change if a different amino acid replaced one of yours.

Answers will vary depending on the amino acids you change.